PhyloDat’AIDS

At a glance

Geospatial distribution

Sampling by region

All territories with background

All territories without background

France (mainland)

Global Network analyses

Cluster start date is defined as join date when the 3rd participant joins clusters. Not terribly important in our analysis, more important in time-to-event analyses.

\[ NormalizedClusterGrowth_{PastYear} = \frac{{ClusterGrowth}_{PastYear}}{\sqrt{ClusterSize}_{PastYear}} \]

To account for the size of the cluster, I normalized cluster growth by the square root of cluster size. For example, the cluster size for a given cluster in the past year is the size of the cluster at the beginning of the year, before any any have been added.

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 2,295/13,538, i.e. 17%.

Cluster size and composition

Overall

By dispersal

Demographics by clustering status

Characteristic Overall
N = 13,538
1
Clusters size ≥3
N = 1,363
1
Singletons
N = 12,175
1
p-value2
sex


<0.001
    Female 4,034 (30%) 107 (7.9%) 3,927 (32%)
    Male 9,392 (69%) 1,247 (91%) 8,145 (67%)
    Transgender F/M 2 (<0.1%) 0 (0%) 2 (<0.1%)
    Transgender M/F 110 (0.8%) 9 (0.7%) 101 (0.8%)
Age 51 (40, 59) 42 (33, 53) 51 (41, 60) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 351 (2.6%) 68 (5.0%) 283 (2.3%)
    ≥25-<35 1,699 (13%) 313 (23%) 1,386 (11%)
    ≥35-<45 2,759 (20%) 377 (28%) 2,382 (20%)
    ≥45-<55 3,402 (25%) 322 (24%) 3,080 (25%)
    ≥55-<80 5,154 (38%) 275 (20%) 4,879 (40%)
    ≥80 173 (1.3%) 8 (0.6%) 165 (1.4%)
WHO region (origin)



    WHO Africa 2,445 (20%) 61 (4.8%) 2,384 (22%)
    WHO Americas 725 (5.9%) 33 (2.6%) 692 (6.3%)
    WHO Eastern Mediterranean 283 (2.3%) 20 (1.6%) 263 (2.4%)
    WHO Europe 8,684 (71%) 1,150 (91%) 7,534 (69%)
    WHO South-East Asia 43 (0.4%) 1 (<0.1%) 42 (0.4%)
    WHO Western Pacific 72 (0.6%) 2 (0.2%) 70 (0.6%)
Regions francaises



    Auvergne-Rhône-Alpes 303 (2.2%) 23 (1.7%) 280 (2.3%)
    Bourgogne-Franche-Comté 18 (0.1%) 3 (0.2%) 15 (0.1%)
    Bretagne 1,256 (9.3%) 102 (7.5%) 1,154 (9.5%)
    Centre-Val de Loire 26 (0.2%) 4 (0.3%) 22 (0.2%)
    Corse 34 (0.3%) 2 (0.1%) 32 (0.3%)
    Grand Est 12 (<0.1%) 0 (0%) 12 (<0.1%)
    Guadeloupe 645 (4.8%) 47 (3.4%) 598 (4.9%)
    Guyane française 8 (<0.1%) 0 (0%) 8 (<0.1%)
    Hauts-de-France 29 (0.2%) 3 (0.2%) 26 (0.2%)
    Île-de-France 160 (1.2%) 12 (0.9%) 148 (1.2%)
    Martinique 922 (6.8%) 99 (7.3%) 823 (6.8%)
    Mayotte 1 (<0.1%) 0 (0%) 1 (<0.1%)
    Normandie 690 (5.1%) 53 (3.9%) 637 (5.2%)
    Nouvelle-Aquitaine 154 (1.1%) 24 (1.8%) 130 (1.1%)
    Occitanie 3,626 (27%) 428 (31%) 3,198 (26%)
    Pays de la Loire 2,863 (21%) 260 (19%) 2,603 (21%)
    Provence-Alpes-Côte-d'Azur 2,787 (21%) 302 (22%) 2,485 (20%)
    Réunion 4 (<0.1%) 1 (<0.1%) 3 (<0.1%)
Primo-infection


<0.001
    Non 12,295 (91%) 1,042 (76%) 11,253 (92%)
    Oui 1,243 (9.2%) 321 (24%) 922 (7.6%)
Transmission risk


<0.001
    Bisexual 737 (5.4%) 113 (8.3%) 624 (5.1%)
    Blood 237 (1.8%) 12 (0.9%) 225 (1.8%)
    Heterosexual 5,786 (43%) 249 (18%) 5,537 (45%)
    IDU 887 (6.6%) 36 (2.6%) 851 (7.0%)
    Mother to child transmission 221 (1.6%) 1 (<0.1%) 220 (1.8%)
    MSM 5,028 (37%) 918 (67%) 4,110 (34%)
    Others 81 (0.6%) 5 (0.4%) 76 (0.6%)
    Unknown 561 (4.1%) 29 (2.1%) 532 (4.4%)
Drug use


<0.001
    Current 1,228 (10%) 221 (18%) 1,007 (9.2%)
    None 6,765 (56%) 616 (49%) 6,149 (56%)
    Past 1,310 (11%) 135 (11%) 1,175 (11%)
    Sometimes 575 (4.7%) 113 (9.0%) 462 (4.2%)
    Substitution 180 (1.5%) 9 (0.7%) 171 (1.6%)
    Unknown 2,118 (17%) 162 (13%) 1,956 (18%)
Baseline HIV RNA level (log10) 4.80 (4.11, 5.44) 4.95 (4.34, 5.64) 4.78 (4.07, 5.42)
Baseline CD4 count 380 (203, 572) 475 (324, 651) 362 (180, 556) <0.001
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Wilcoxon rank sum test; Pearson’s Chi-squared test

Network analyses by region

Pays de la Loire

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 434/2,863, i.e. 15%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 831 distinct clusters including 25% of local clusters ( 20 400% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 2,863
1
Clusters size ≥3
N = 260
1
Dyads
N = 174
1
Singletons
N = 2,429
1
p-value2
sex




    Female 965 (34%) 27 (10%) 47 (27%) 891 (37%)
    Male 1,887 (66%) 232 (89%) 127 (73%) 1,528 (63%)
    Transgender M/F 11 (0.4%) 1 (0.4%) 0 (0%) 10 (0.4%)
Age 51 (41, 60) 47 (38, 56) 46 (36, 57) 52 (41, 60) <0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 55 (1.9%) 3 (1.2%) 4 (2.3%) 48 (2.0%)
    ≥25-<35 333 (12%) 44 (17%) 32 (18%) 257 (11%)
    ≥35-<45 572 (20%) 65 (25%) 47 (27%) 460 (19%)
    ≥45-<55 744 (26%) 74 (28%) 39 (22%) 631 (26%)
    ≥55-<80 1,131 (40%) 71 (27%) 52 (30%) 1,008 (41%)
    ≥80 28 (1.0%) 3 (1.2%) 0 (0%) 25 (1.0%)
WHO region (origin)




    WHO Africa 829 (30%) 15 (5.8%) 51 (30%) 763 (32%)
    WHO Americas 69 (2.5%) 4 (1.5%) 3 (1.8%) 62 (2.6%)
    WHO Eastern Mediterranean 56 (2.0%) 2 (0.8%) 4 (2.4%) 50 (2.1%)
    WHO Europe 1,821 (65%) 237 (91%) 111 (66%) 1,473 (62%)
    WHO South-East Asia 11 (0.4%) 0 (0%) 0 (0%) 11 (0.5%)
    WHO Western Pacific 22 (0.8%) 2 (0.8%) 0 (0%) 20 (0.8%)
Primo-infection



<0.001
    Non 2,659 (93%) 199 (77%) 158 (91%) 2,302 (95%)
    Oui 204 (7.1%) 61 (23%) 16 (9.2%) 127 (5.2%)
Transmission risk




    Bisexual 128 (4.5%) 16 (6.2%) 8 (4.6%) 104 (4.3%)
    Blood 60 (2.1%) 2 (0.8%) 2 (1.1%) 56 (2.3%)
    Heterosexual 1,335 (47%) 53 (20%) 77 (44%) 1,205 (50%)
    IDU 141 (4.9%) 4 (1.5%) 8 (4.6%) 129 (5.3%)
    Mother to child transmission 53 (1.9%) 0 (0%) 3 (1.7%) 50 (2.1%)
    MSM 1,039 (36%) 182 (70%) 69 (40%) 788 (32%)
    Others 13 (0.5%) 1 (0.4%) 1 (0.6%) 11 (0.5%)
    Unknown 94 (3.3%) 2 (0.8%) 6 (3.4%) 86 (3.5%)
Drug use




    Current 236 (8.6%) 40 (16%) 20 (12%) 176 (7.6%)
    None 1,875 (68%) 160 (63%) 103 (61%) 1,612 (69%)
    Past 261 (9.5%) 20 (7.8%) 18 (11%) 223 (9.6%)
    Sometimes 147 (5.3%) 28 (11%) 13 (7.6%) 106 (4.6%)
    Substitution 26 (0.9%) 2 (0.8%) 2 (1.2%) 22 (0.9%)
    Unknown 207 (7.5%) 5 (2.0%) 14 (8.2%) 188 (8.1%)
Baseline HIV RNA level (log10) 4.80 (4.09, 5.42) 4.87 (4.39, 5.66) 4.86 (3.96, 5.49) 4.76 (4.07, 5.39) 0.002
Baseline CD4 count 366 (190, 558) 438 (317, 613) 414 (218, 585) 344 (173, 543) <0.001
1 n (%); Median (Q1, Q3)
2 Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 2,429
1
Not Growing
N = 355
1
Growing
N = 79
1
p-value2
sex


<0.001
    Female 891 (37%) 70 (20%) 4 (5.1%)
    Male 1,528 (63%) 284 (80%) 75 (95%)
    Transgender M/F 10 (0.4%) 1 (0.3%) 0 (0%)
Age 52 (41, 60) 44 (35, 54) 53 (47, 61) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 48 (2.0%) 6 (1.7%) 1 (1.3%)
    ≥25-<35 257 (11%) 76 (21%) 0 (0%)
    ≥35-<45 460 (19%) 99 (28%) 13 (16%)
    ≥45-<55 631 (26%) 86 (24%) 27 (34%)
    ≥55-<80 1,008 (41%) 87 (25%) 36 (46%)
    ≥80 25 (1.0%) 1 (0.3%) 2 (2.5%)
WHO region (origin)



    WHO Africa 763 (32%) 65 (19%) 1 (1.3%)
    WHO Americas 62 (2.6%) 7 (2.0%) 0 (0%)
    WHO Eastern Mediterranean 50 (2.1%) 6 (1.7%) 0 (0%)
    WHO Europe 1,473 (62%) 271 (77%) 77 (97%)
    WHO South-East Asia 11 (0.5%) 0 (0%) 0 (0%)
    WHO Western Pacific 20 (0.8%) 1 (0.3%) 1 (1.3%)
Primo-infection


<0.001
    Non 2,302 (95%) 296 (83%) 61 (77%)
    Oui 127 (5.2%) 59 (17%) 18 (23%)
Transmission risk



    Bisexual 104 (4.3%) 19 (5.4%) 5 (6.3%)
    Blood 56 (2.3%) 2 (0.6%) 2 (2.5%)
    Heterosexual 1,205 (50%) 117 (33%) 13 (16%)
    IDU 129 (5.3%) 10 (2.8%) 2 (2.5%)
    Mother to child transmission 50 (2.1%) 3 (0.8%) 0 (0%)
    MSM 788 (32%) 195 (55%) 56 (71%)
    Others 11 (0.5%) 1 (0.3%) 1 (1.3%)
    Unknown 86 (3.5%) 8 (2.3%) 0 (0%)
Drug use



    Current 176 (7.6%) 51 (15%) 9 (12%)
    None 1,612 (69%) 209 (60%) 54 (69%)
    Past 223 (9.6%) 31 (8.9%) 7 (9.0%)
    Sometimes 106 (4.6%) 34 (9.8%) 7 (9.0%)
    Substitution 22 (0.9%) 4 (1.2%) 0 (0%)
    Unknown 188 (8.1%) 18 (5.2%) 1 (1.3%)
Baseline HIV RNA level (log10) 4.76 (4.07, 5.39) 4.86 (4.23, 5.59) 4.95 (4.62, 5.54) 0.003
Baseline CD4 count 344 (173, 543) 436 (271, 614) 432 (310, 537) <0.001
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Table of cluster dispersal

Characteristic local only
N = 204
1
Not clustering
N = 2,429
1
spread
N = 230
1
p-value2
sex



    Female 39 (19%) 891 (37%) 35 (15%)
    Male 164 (80%) 1,528 (63%) 195 (85%)
    Transgender M/F 1 (0.5%) 10 (0.4%) 0 (0%)
Age 48 (38, 57) 52 (41, 60) 44 (36, 55) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 3 (1.5%) 48 (2.0%) 4 (1.7%)
    ≥25-<35 31 (15%) 257 (11%) 45 (20%)
    ≥35-<45 42 (21%) 460 (19%) 70 (30%)
    ≥45-<55 61 (30%) 631 (26%) 52 (23%)
    ≥55-<80 65 (32%) 1,008 (41%) 58 (25%)
    ≥80 2 (1.0%) 25 (1.0%) 1 (0.4%)
WHO region (origin)



    WHO Africa 42 (21%) 763 (32%) 24 (11%)
    WHO Americas 3 (1.5%) 62 (2.6%) 4 (1.8%)
    WHO Eastern Mediterranean 2 (1.0%) 50 (2.1%) 4 (1.8%)
    WHO Europe 154 (76%) 1,473 (62%) 194 (86%)
    WHO South-East Asia 0 (0%) 11 (0.5%) 0 (0%)
    WHO Western Pacific 2 (1.0%) 20 (0.8%) 0 (0%)
Primo-infection


<0.001
    Non 176 (86%) 2,302 (95%) 181 (79%)
    Oui 28 (14%) 127 (5.2%) 49 (21%)
Transmission risk



    Bisexual 14 (6.9%) 104 (4.3%) 10 (4.3%)
    Blood 2 (1.0%) 56 (2.3%) 2 (0.9%)
    Heterosexual 76 (37%) 1,205 (50%) 54 (23%)
    IDU 3 (1.5%) 129 (5.3%) 9 (3.9%)
    Mother to child transmission 3 (1.5%) 50 (2.1%) 0 (0%)
    MSM 100 (49%) 788 (32%) 151 (66%)
    Others 1 (0.5%) 11 (0.5%) 1 (0.4%)
    Unknown 5 (2.5%) 86 (3.5%) 3 (1.3%)
Drug use



    Current 32 (16%) 176 (7.6%) 28 (12%)
    None 121 (61%) 1,612 (69%) 142 (63%)
    Past 14 (7.1%) 223 (9.6%) 24 (11%)
    Sometimes 18 (9.1%) 106 (4.6%) 23 (10%)
    Substitution 1 (0.5%) 22 (0.9%) 3 (1.3%)
    Unknown 12 (6.1%) 188 (8.1%) 7 (3.1%)
Baseline HIV RNA level (log10) 4.86 (4.20, 5.49) 4.76 (4.07, 5.39) 4.88 (4.38, 5.78) 0.002
Baseline CD4 count 414 (219, 618) 344 (173, 543) 447 (334, 586) <0.001
1 n (%); Median (Q1, Q3)
2 Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Occitanie

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 667/3,626, i.e. 18%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 1018 distinct clusters including 31% of local clusters ( 31 900% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 3,626
1
Clusters size ≥3
N = 428
1
Dyads
N = 239
1
Singletons
N = 2,959
1
p-value2
sex




    Female 898 (25%) 15 (3.5%) 35 (15%) 848 (29%)
    Male 2,712 (75%) 410 (96%) 201 (84%) 2,101 (71%)
    Transgender M/F 16 (0.4%) 3 (0.7%) 3 (1.3%) 10 (0.3%)
Age 49 (39, 59) 41 (32, 50) 44 (36, 53) 51 (40, 60) <0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 97 (2.7%) 21 (4.9%) 5 (2.1%) 71 (2.4%)
    ≥25-<35 457 (13%) 106 (25%) 41 (17%) 310 (10%)
    ≥35-<45 814 (22%) 136 (32%) 74 (31%) 604 (20%)
    ≥45-<55 968 (27%) 99 (23%) 72 (30%) 797 (27%)
    ≥55-<80 1,245 (34%) 63 (15%) 47 (20%) 1,135 (38%)
    ≥80 45 (1.2%) 3 (0.7%) 0 (0%) 42 (1.4%)
WHO region (origin)




    WHO Africa 635 (19%) 20 (4.9%) 28 (12%) 587 (21%)
    WHO Americas 94 (2.8%) 9 (2.2%) 11 (4.9%) 74 (2.7%)
    WHO Eastern Mediterranean 106 (3.1%) 9 (2.2%) 8 (3.5%) 89 (3.2%)
    WHO Europe 2,541 (74%) 371 (91%) 178 (79%) 1,992 (72%)
    WHO South-East Asia 16 (0.5%) 0 (0%) 1 (0.4%) 15 (0.5%)
    WHO Western Pacific 20 (0.6%) 0 (0%) 0 (0%) 20 (0.7%)
Primo-infection



<0.001
    Non 3,194 (88%) 314 (73%) 195 (82%) 2,685 (91%)
    Oui 432 (12%) 114 (27%) 44 (18%) 274 (9.3%)
Transmission risk




    Bisexual 168 (4.6%) 22 (5.1%) 14 (5.9%) 132 (4.5%)
    Blood 61 (1.7%) 3 (0.7%) 2 (0.8%) 56 (1.9%)
    Heterosexual 1,203 (33%) 38 (8.9%) 58 (24%) 1,107 (37%)
    IDU 199 (5.5%) 7 (1.6%) 11 (4.6%) 181 (6.1%)
    Mother to child transmission 52 (1.4%) 0 (0%) 3 (1.3%) 49 (1.7%)
    MSM 1,653 (46%) 338 (79%) 141 (59%) 1,174 (40%)
    Others 29 (0.8%) 3 (0.7%) 2 (0.8%) 24 (0.8%)
    Unknown 261 (7.2%) 17 (4.0%) 8 (3.3%) 236 (8.0%)
Drug use




    Current 328 (11%) 65 (17%) 27 (13%) 236 (9.3%)
    None 1,923 (62%) 194 (51%) 122 (57%) 1,607 (64%)
    Past 351 (11%) 36 (9.5%) 25 (12%) 290 (11%)
    Sometimes 296 (9.5%) 65 (17%) 27 (13%) 204 (8.1%)
    Substitution 45 (1.4%) 3 (0.8%) 3 (1.4%) 39 (1.5%)
    Unknown 174 (5.6%) 14 (3.7%) 10 (4.7%) 150 (5.9%)
Baseline HIV RNA level (log10) 4.92 (4.27, 5.59) 5.07 (4.52, 5.79) 4.91 (4.38, 5.56) 4.88 (4.19, 5.57) <0.001
Baseline CD4 count 392 (202, 581) 478 (332, 665) 455 (319, 613) 351 (166, 555) <0.001
1 n (%); Median (Q1, Q3)
2 Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 2,959
1
Not Growing
N = 635
1
Growing
N = 32
1
p-value2
sex


<0.001
    Female 848 (29%) 47 (7.4%) 3 (9.4%)
    Male 2,101 (71%) 582 (92%) 29 (91%)
    Transgender M/F 10 (0.3%) 6 (0.9%) 0 (0%)
Age 51 (40, 60) 42 (34, 51) 52 (45, 58) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 71 (2.4%) 26 (4.1%) 0 (0%)
    ≥25-<35 310 (10%) 143 (23%) 4 (13%)
    ≥35-<45 604 (20%) 207 (33%) 3 (9.4%)
    ≥45-<55 797 (27%) 157 (25%) 14 (44%)
    ≥55-<80 1,135 (38%) 100 (16%) 10 (31%)
    ≥80 42 (1.4%) 2 (0.3%) 1 (3.1%)
WHO region (origin)



    WHO Africa 587 (21%) 47 (7.8%) 1 (3.3%)
    WHO Americas 74 (2.7%) 20 (3.3%) 0 (0%)
    WHO Eastern Mediterranean 89 (3.2%) 17 (2.8%) 0 (0%)
    WHO Europe 1,992 (72%) 520 (86%) 29 (97%)
    WHO South-East Asia 15 (0.5%) 1 (0.2%) 0 (0%)
    WHO Western Pacific 20 (0.7%) 0 (0%) 0 (0%)
Primo-infection


<0.001
    Non 2,685 (91%) 483 (76%) 26 (81%)
    Oui 274 (9.3%) 152 (24%) 6 (19%)
Transmission risk



    Bisexual 132 (4.5%) 36 (5.7%) 0 (0%)
    Blood 56 (1.9%) 4 (0.6%) 1 (3.1%)
    Heterosexual 1,107 (37%) 92 (14%) 4 (13%)
    IDU 181 (6.1%) 16 (2.5%) 2 (6.3%)
    Mother to child transmission 49 (1.7%) 3 (0.5%) 0 (0%)
    MSM 1,174 (40%) 455 (72%) 24 (75%)
    Others 24 (0.8%) 5 (0.8%) 0 (0%)
    Unknown 236 (8.0%) 24 (3.8%) 1 (3.1%)
Drug use



    Current 236 (9.3%) 89 (16%) 3 (10%)
    None 1,607 (64%) 296 (53%) 20 (69%)
    Past 290 (11%) 59 (10%) 2 (6.9%)
    Sometimes 204 (8.1%) 89 (16%) 3 (10%)
    Substitution 39 (1.5%) 6 (1.1%) 0 (0%)
    Unknown 150 (5.9%) 23 (4.1%) 1 (3.4%)
Baseline HIV RNA level (log10) 4.88 (4.19, 5.57) 5.03 (4.46, 5.69) 5.00 (4.34, 5.43) <0.001
Baseline CD4 count 351 (166, 555) 472 (331, 652) 613 (257, 702) <0.001
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 319
1
Not clustering
N = 2,959
1
spread
N = 348
1
p-value2
sex



    Female 27 (8.5%) 848 (29%) 23 (6.6%)
    Male 287 (90%) 2,101 (71%) 324 (93%)
    Transgender M/F 5 (1.6%) 10 (0.3%) 1 (0.3%)
Age 44 (36, 52) 51 (40, 60) 41 (32, 51) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 5 (1.6%) 71 (2.4%) 21 (6.0%)
    ≥25-<35 60 (19%) 310 (10%) 87 (25%)
    ≥35-<45 104 (33%) 604 (20%) 106 (30%)
    ≥45-<55 94 (29%) 797 (27%) 77 (22%)
    ≥55-<80 55 (17%) 1,135 (38%) 55 (16%)
    ≥80 1 (0.3%) 42 (1.4%) 2 (0.6%)
WHO region (origin)



    WHO Africa 33 (11%) 587 (21%) 15 (4.6%)
    WHO Americas 14 (4.5%) 74 (2.7%) 6 (1.9%)
    WHO Eastern Mediterranean 10 (3.2%) 89 (3.2%) 7 (2.2%)
    WHO Europe 253 (81%) 1,992 (72%) 296 (91%)
    WHO South-East Asia 1 (0.3%) 15 (0.5%) 0 (0%)
    WHO Western Pacific 0 (0%) 20 (0.7%) 0 (0%)
Primo-infection


<0.001
    Non 240 (75%) 2,685 (91%) 269 (77%)
    Oui 79 (25%) 274 (9.3%) 79 (23%)
Transmission risk



    Bisexual 19 (6.0%) 132 (4.5%) 17 (4.9%)
    Blood 2 (0.6%) 56 (1.9%) 3 (0.9%)
    Heterosexual 61 (19%) 1,107 (37%) 35 (10%)
    IDU 6 (1.9%) 181 (6.1%) 12 (3.4%)
    Mother to child transmission 1 (0.3%) 49 (1.7%) 2 (0.6%)
    MSM 215 (67%) 1,174 (40%) 264 (76%)
    Others 5 (1.6%) 24 (0.8%) 0 (0%)
    Unknown 10 (3.1%) 236 (8.0%) 15 (4.3%)
Drug use



    Current 44 (15%) 236 (9.3%) 48 (16%)
    None 168 (58%) 1,607 (64%) 148 (49%)
    Past 21 (7.3%) 290 (11%) 40 (13%)
    Sometimes 45 (16%) 204 (8.1%) 47 (16%)
    Substitution 3 (1.0%) 39 (1.5%) 3 (1.0%)
    Unknown 7 (2.4%) 150 (5.9%) 17 (5.6%)
Baseline HIV RNA level (log10) 4.98 (4.44, 5.56) 4.88 (4.19, 5.57) 5.08 (4.52, 5.79) <0.001
Baseline CD4 count 465 (328, 632) 351 (166, 555) 477 (340, 662) <0.001
1 n (%); Median (Q1, Q3)
2 Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Bretagne

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 175/1,256, i.e. 14%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 508 distinct clusters including 11% of local clusters ( 5 600% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 1,256
1
Clusters size ≥3
N = 102
1
Dyads
N = 73
1
Singletons
N = 1,081
1
p-value2
sex



<0.001
    Female 428 (34%) 7 (6.9%) 16 (22%) 405 (37%)
    Male 822 (65%) 94 (92%) 57 (78%) 671 (62%)
    Transgender F/M 1 (<0.1%) 0 (0%) 0 (0%) 1 (<0.1%)
    Transgender M/F 5 (0.4%) 1 (1.0%) 0 (0%) 4 (0.4%)
Age 52 (41, 60) 44 (36, 54) 43 (38, 51) 53 (43, 61) <0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 38 (3.0%) 5 (4.9%) 5 (6.8%) 28 (2.6%)
    ≥25-<35 129 (10%) 18 (18%) 9 (12%) 102 (9.4%)
    ≥35-<45 245 (20%) 32 (31%) 27 (37%) 186 (17%)
    ≥45-<55 310 (25%) 24 (24%) 19 (26%) 267 (25%)
    ≥55-<80 518 (41%) 23 (23%) 13 (18%) 482 (45%)
    ≥80 16 (1.3%) 0 (0%) 0 (0%) 16 (1.5%)
WHO region (origin)




    WHO Africa 290 (24%) 6 (5.9%) 7 (9.7%) 277 (26%)
    WHO Americas 33 (2.7%) 1 (1.0%) 4 (5.6%) 28 (2.7%)
    WHO Eastern Mediterranean 9 (0.7%) 1 (1.0%) 0 (0%) 8 (0.8%)
    WHO Europe 887 (72%) 93 (92%) 61 (85%) 733 (69%)
    WHO South-East Asia 3 (0.2%) 0 (0%) 0 (0%) 3 (0.3%)
    WHO Western Pacific 7 (0.6%) 0 (0%) 0 (0%) 7 (0.7%)
Primo-infection



<0.001
    Non 1,183 (94%) 80 (78%) 66 (90%) 1,037 (96%)
    Oui 73 (5.8%) 22 (22%) 7 (9.6%) 44 (4.1%)
Transmission risk




    Bisexual 58 (4.6%) 14 (14%) 1 (1.4%) 43 (4.0%)
    Blood 27 (2.1%) 2 (2.0%) 1 (1.4%) 24 (2.2%)
    Heterosexual 563 (45%) 14 (14%) 24 (33%) 525 (49%)
    IDU 72 (5.7%) 4 (3.9%) 4 (5.5%) 64 (5.9%)
    Mother to child transmission 27 (2.1%) 0 (0%) 0 (0%) 27 (2.5%)
    MSM 438 (35%) 63 (62%) 40 (55%) 335 (31%)
    Others 15 (1.2%) 1 (1.0%) 1 (1.4%) 13 (1.2%)
    Unknown 56 (4.5%) 4 (3.9%) 2 (2.7%) 50 (4.6%)
Drug use




    Current 90 (9.0%) 19 (23%) 10 (16%) 61 (7.2%)
    None 425 (43%) 33 (40%) 27 (42%) 365 (43%)
    Past 74 (7.4%) 5 (6.0%) 7 (11%) 62 (7.3%)
    Sometimes 23 (2.3%) 1 (1.2%) 3 (4.7%) 19 (2.2%)
    Substitution 22 (2.2%) 3 (3.6%) 1 (1.6%) 18 (2.1%)
    Unknown 361 (36%) 22 (27%) 16 (25%) 323 (38%)
Baseline HIV RNA level (log10) 4.87 (4.13, 5.48) 5.12 (4.55, 6.01) 5.00 (4.63, 5.53) 4.80 (4.07, 5.45) <0.001
Baseline CD4 count 353 (180, 548) 404 (261, 606) 424 (274, 637) 331 (158, 537) 0.003
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 1,081
1
Not Growing
N = 159
1
Growing
N = 16
1
p-value2
sex


<0.001
    Female 405 (37%) 21 (13%) 2 (13%)
    Male 671 (62%) 137 (86%) 14 (88%)
    Transgender F/M 1 (<0.1%) 0 (0%) 0 (0%)
    Transgender M/F 4 (0.4%) 1 (0.6%) 0 (0%)
Age 53 (43, 61) 43 (35, 53) 46 (39, 51) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 28 (2.6%) 10 (6.3%) 0 (0%)
    ≥25-<35 102 (9.4%) 27 (17%) 0 (0%)
    ≥35-<45 186 (17%) 52 (33%) 7 (44%)
    ≥45-<55 267 (25%) 37 (23%) 6 (38%)
    ≥55-<80 482 (45%) 33 (21%) 3 (19%)
    ≥80 16 (1.5%) 0 (0%) 0 (0%)
WHO region (origin)



    WHO Africa 277 (26%) 13 (8.3%) 0 (0%)
    WHO Americas 28 (2.7%) 5 (3.2%) 0 (0%)
    WHO Eastern Mediterranean 8 (0.8%) 1 (0.6%) 0 (0%)
    WHO Europe 733 (69%) 138 (88%) 16 (100%)
    WHO South-East Asia 3 (0.3%) 0 (0%) 0 (0%)
    WHO Western Pacific 7 (0.7%) 0 (0%) 0 (0%)
Primo-infection


<0.001
    Non 1,037 (96%) 132 (83%) 14 (88%)
    Oui 44 (4.1%) 27 (17%) 2 (13%)
Transmission risk



    Bisexual 43 (4.0%) 11 (6.9%) 4 (25%)
    Blood 24 (2.2%) 3 (1.9%) 0 (0%)
    Heterosexual 525 (49%) 35 (22%) 3 (19%)
    IDU 64 (5.9%) 6 (3.8%) 2 (13%)
    Mother to child transmission 27 (2.5%) 0 (0%) 0 (0%)
    MSM 335 (31%) 96 (60%) 7 (44%)
    Others 13 (1.2%) 2 (1.3%) 0 (0%)
    Unknown 50 (4.6%) 6 (3.8%) 0 (0%)
Drug use



    Current 61 (7.2%) 25 (19%) 4 (29%)
    None 365 (43%) 56 (42%) 4 (29%)
    Past 62 (7.3%) 9 (6.8%) 3 (21%)
    Sometimes 19 (2.2%) 4 (3.0%) 0 (0%)
    Substitution 18 (2.1%) 3 (2.3%) 1 (7.1%)
    Unknown 323 (38%) 36 (27%) 2 (14%)
Baseline HIV RNA level (log10) 4.80 (4.07, 5.45) 5.08 (4.59, 5.80) 5.45 (4.26, 5.63) <0.001
Baseline CD4 count 331 (158, 537) 416 (259, 589) 796 (294, 899) <0.001
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 56
1
Not clustering
N = 1,081
1
spread
N = 119
1
p-value2
sex


<0.001
    Female 12 (21%) 405 (37%) 11 (9.2%)
    Male 44 (79%) 671 (62%) 107 (90%)
    Transgender F/M 0 (0%) 1 (<0.1%) 0 (0%)
    Transgender M/F 0 (0%) 4 (0.4%) 1 (0.8%)
Age 43 (37, 51) 53 (43, 61) 44 (36, 54) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 2 (3.6%) 28 (2.6%) 8 (6.7%)
    ≥25-<35 9 (16%) 102 (9.4%) 18 (15%)
    ≥35-<45 21 (38%) 186 (17%) 38 (32%)
    ≥45-<55 15 (27%) 267 (25%) 28 (24%)
    ≥55-<80 9 (16%) 482 (45%) 27 (23%)
    ≥80 0 (0%) 16 (1.5%) 0 (0%)
WHO region (origin)



    WHO Africa 5 (9.1%) 277 (26%) 8 (6.8%)
    WHO Americas 3 (5.5%) 28 (2.7%) 2 (1.7%)
    WHO Eastern Mediterranean 0 (0%) 8 (0.8%) 1 (0.8%)
    WHO Europe 47 (85%) 733 (69%) 107 (91%)
    WHO South-East Asia 0 (0%) 3 (0.3%) 0 (0%)
    WHO Western Pacific 0 (0%) 7 (0.7%) 0 (0%)
Primo-infection


<0.001
    Non 51 (91%) 1,037 (96%) 95 (80%)
    Oui 5 (8.9%) 44 (4.1%) 24 (20%)
Transmission risk



    Bisexual 1 (1.8%) 43 (4.0%) 14 (12%)
    Blood 2 (3.6%) 24 (2.2%) 1 (0.8%)
    Heterosexual 17 (30%) 525 (49%) 21 (18%)
    IDU 5 (8.9%) 64 (5.9%) 3 (2.5%)
    Mother to child transmission 0 (0%) 27 (2.5%) 0 (0%)
    MSM 28 (50%) 335 (31%) 75 (63%)
    Others 1 (1.8%) 13 (1.2%) 1 (0.8%)
    Unknown 2 (3.6%) 50 (4.6%) 4 (3.4%)
Drug use



    Current 12 (24%) 61 (7.2%) 17 (18%)
    None 20 (39%) 365 (43%) 40 (42%)
    Past 5 (9.8%) 62 (7.3%) 7 (7.3%)
    Sometimes 2 (3.9%) 19 (2.2%) 2 (2.1%)
    Substitution 2 (3.9%) 18 (2.1%) 2 (2.1%)
    Unknown 10 (20%) 323 (38%) 28 (29%)
Baseline HIV RNA level (log10) 4.98 (4.55, 5.40) 4.80 (4.07, 5.45) 5.15 (4.64, 5.94) <0.001
Baseline CD4 count 446 (259, 665) 331 (158, 537) 415 (273, 590) 0.003
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Provence-Alpes-Côte-d’Azur

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 519/2,787, i.e. 19%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 844 distinct clusters including 39% of local clusters ( 32 800% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 2,787
1
Clusters size ≥3
N = 302
1
Dyads
N = 217
1
Singletons
N = 2,268
1
p-value2
sex




    Female 728 (26%) 21 (7.0%) 38 (18%) 669 (29%)
    Male 2,005 (72%) 277 (92%) 175 (81%) 1,553 (68%)
    Transgender M/F 54 (1.9%) 4 (1.3%) 4 (1.8%) 46 (2.0%)
Age 52 (41, 60) 42 (34, 54) 45 (35, 55) 54 (43, 60) <0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 59 (2.1%) 18 (6.0%) 12 (5.5%) 29 (1.3%)
    ≥25-<35 307 (11%) 62 (21%) 41 (19%) 204 (9.0%)
    ≥35-<45 545 (20%) 90 (30%) 53 (24%) 402 (18%)
    ≥45-<55 671 (24%) 61 (20%) 54 (25%) 556 (25%)
    ≥55-<80 1,179 (42%) 70 (23%) 56 (26%) 1,053 (46%)
    ≥80 26 (0.9%) 1 (0.3%) 1 (0.5%) 24 (1.1%)
WHO region (origin)




    WHO Africa 308 (16%) 11 (4.7%) 27 (18%) 270 (18%)
    WHO Americas 118 (6.1%) 8 (3.4%) 6 (3.9%) 104 (6.8%)
    WHO Eastern Mediterranean 89 (4.6%) 6 (2.6%) 8 (5.2%) 75 (4.9%)
    WHO Europe 1,382 (72%) 209 (89%) 110 (71%) 1,063 (69%)
    WHO South-East Asia 7 (0.4%) 1 (0.4%) 0 (0%) 6 (0.4%)
    WHO Western Pacific 18 (0.9%) 0 (0%) 3 (1.9%) 15 (1.0%)
Primo-infection



<0.001
    Non 2,555 (92%) 242 (80%) 195 (90%) 2,118 (93%)
    Oui 232 (8.3%) 60 (20%) 22 (10%) 150 (6.6%)
Transmission risk




    Bisexual 123 (4.4%) 19 (6.3%) 9 (4.1%) 95 (4.2%)
    Blood 44 (1.6%) 2 (0.7%) 2 (0.9%) 40 (1.8%)
    Heterosexual 992 (36%) 52 (17%) 54 (25%) 886 (39%)
    IDU 392 (14%) 18 (6.0%) 15 (6.9%) 359 (16%)
    Mother to child transmission 51 (1.8%) 0 (0%) 5 (2.3%) 46 (2.0%)
    MSM 1,109 (40%) 209 (69%) 125 (58%) 775 (34%)
    Others 11 (0.4%) 0 (0%) 1 (0.5%) 10 (0.4%)
    Unknown 65 (2.3%) 2 (0.7%) 6 (2.8%) 57 (2.5%)
Drug use




    Current 300 (11%) 56 (19%) 32 (15%) 212 (9.5%)
    None 788 (29%) 77 (26%) 68 (33%) 643 (29%)
    Past 335 (12%) 46 (16%) 22 (11%) 267 (12%)
    Sometimes 33 (1.2%) 5 (1.7%) 2 (1.0%) 26 (1.2%)
    Substitution 55 (2.0%) 0 (0%) 3 (1.4%) 52 (2.3%)
    Unknown 1,215 (45%) 111 (38%) 80 (39%) 1,024 (46%)
Baseline HIV RNA level (log10) 4.81 (4.08, 5.46) 4.93 (4.24, 5.54) 4.82 (4.07, 5.30) 4.79 (4.00, 5.47) 0.074
Baseline CD4 count 410 (247, 592) 504 (352, 688) 480 (330, 625) 368 (205, 556) <0.001
1 n (%); Median (Q1, Q3)
2 Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 2,268
1
Not Growing
N = 505
1
Growing
N = 14
1
p-value2
sex


<0.001
    Female 669 (29%) 56 (11%) 3 (21%)
    Male 1,553 (68%) 442 (88%) 10 (71%)
    Transgender M/F 46 (2.0%) 7 (1.4%) 1 (7.1%)
Age 54 (43, 60) 43 (34, 53) 60 (56, 65) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 29 (1.3%) 30 (5.9%) 0 (0%)
    ≥25-<35 204 (9.0%) 103 (20%) 0 (0%)
    ≥35-<45 402 (18%) 143 (28%) 0 (0%)
    ≥45-<55 556 (25%) 114 (23%) 1 (7.1%)
    ≥55-<80 1,053 (46%) 113 (22%) 13 (93%)
    ≥80 24 (1.1%) 2 (0.4%) 0 (0%)
WHO region (origin)



    WHO Africa 270 (18%) 38 (10%) 0 (0%)
    WHO Americas 104 (6.8%) 14 (3.7%) 0 (0%)
    WHO Eastern Mediterranean 75 (4.9%) 14 (3.7%) 0 (0%)
    WHO Europe 1,063 (69%) 309 (82%) 10 (100%)
    WHO South-East Asia 6 (0.4%) 1 (0.3%) 0 (0%)
    WHO Western Pacific 15 (1.0%) 3 (0.8%) 0 (0%)
Primo-infection


<0.001
    Non 2,118 (93%) 423 (84%) 14 (100%)
    Oui 150 (6.6%) 82 (16%) 0 (0%)
Transmission risk



    Bisexual 95 (4.2%) 26 (5.1%) 2 (14%)
    Blood 40 (1.8%) 3 (0.6%) 1 (7.1%)
    Heterosexual 886 (39%) 104 (21%) 2 (14%)
    IDU 359 (16%) 26 (5.1%) 7 (50%)
    Mother to child transmission 46 (2.0%) 5 (1.0%) 0 (0%)
    MSM 775 (34%) 332 (66%) 2 (14%)
    Others 10 (0.4%) 1 (0.2%) 0 (0%)
    Unknown 57 (2.5%) 8 (1.6%) 0 (0%)
Drug use



    Current 212 (9.5%) 87 (18%) 1 (7.1%)
    None 643 (29%) 142 (29%) 3 (21%)
    Past 267 (12%) 64 (13%) 4 (29%)
    Sometimes 26 (1.2%) 7 (1.4%) 0 (0%)
    Substitution 52 (2.3%) 3 (0.6%) 0 (0%)
    Unknown 1,024 (46%) 185 (38%) 6 (43%)
Baseline HIV RNA level (log10) 4.79 (4.00, 5.47) 4.86 (4.18, 5.43) 5.04 (4.89, 5.08) 0.2
Baseline CD4 count 368 (205, 556) 484 (345, 659) 238 (221, 240) <0.001
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 328
1
Not clustering
N = 2,268
1
spread
N = 191
1
p-value2
sex



    Female 38 (12%) 669 (29%) 21 (11%)
    Male 287 (88%) 1,553 (68%) 165 (86%)
    Transgender M/F 3 (0.9%) 46 (2.0%) 5 (2.6%)
Age 44 (35, 55) 54 (43, 60) 41 (32, 53) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 17 (5.2%) 29 (1.3%) 13 (6.8%)
    ≥25-<35 55 (17%) 204 (9.0%) 48 (25%)
    ≥35-<45 93 (28%) 402 (18%) 50 (26%)
    ≥45-<55 76 (23%) 556 (25%) 39 (20%)
    ≥55-<80 85 (26%) 1,053 (46%) 41 (21%)
    ≥80 2 (0.6%) 24 (1.1%) 0 (0%)
WHO region (origin)



    WHO Africa 30 (13%) 270 (18%) 8 (5.3%)
    WHO Americas 10 (4.2%) 104 (6.8%) 4 (2.7%)
    WHO Eastern Mediterranean 13 (5.4%) 75 (4.9%) 1 (0.7%)
    WHO Europe 183 (77%) 1,063 (69%) 136 (91%)
    WHO South-East Asia 0 (0%) 6 (0.4%) 1 (0.7%)
    WHO Western Pacific 3 (1.3%) 15 (1.0%) 0 (0%)
Primo-infection


<0.001
    Non 274 (84%) 2,118 (93%) 163 (85%)
    Oui 54 (16%) 150 (6.6%) 28 (15%)
Transmission risk



    Bisexual 18 (5.5%) 95 (4.2%) 10 (5.2%)
    Blood 1 (0.3%) 40 (1.8%) 3 (1.6%)
    Heterosexual 75 (23%) 886 (39%) 31 (16%)
    IDU 16 (4.9%) 359 (16%) 17 (8.9%)
    Mother to child transmission 3 (0.9%) 46 (2.0%) 2 (1.0%)
    MSM 207 (63%) 775 (34%) 127 (66%)
    Others 1 (0.3%) 10 (0.4%) 0 (0%)
    Unknown 7 (2.1%) 57 (2.5%) 1 (0.5%)
Drug use



    Current 51 (16%) 212 (9.5%) 37 (20%)
    None 95 (30%) 643 (29%) 50 (27%)
    Past 39 (12%) 267 (12%) 29 (16%)
    Sometimes 3 (0.9%) 26 (1.2%) 4 (2.2%)
    Substitution 2 (0.6%) 52 (2.3%) 1 (0.5%)
    Unknown 126 (40%) 1,024 (46%) 65 (35%)
Baseline HIV RNA level (log10) 4.76 (4.04, 5.30) 4.79 (4.00, 5.47) 4.99 (4.51, 5.64) 0.005
Baseline CD4 count 484 (342, 644) 368 (205, 556) 481 (325, 682) <0.001
1 n (%); Median (Q1, Q3)
2 Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Normandie

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 102/690, i.e. 15%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 395 distinct clusters including 13% of local clusters ( 5 300% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 690
1
Clusters size ≥3
N = 53
1
Dyads
N = 49
1
Singletons
N = 588
1
p-value2
sex



<0.001
    Female 242 (35%) 5 (9.4%) 8 (16%) 229 (39%)
    Male 431 (62%) 48 (91%) 39 (80%) 344 (59%)
    Transgender F/M 1 (0.1%) 0 (0%) 0 (0%) 1 (0.2%)
    Transgender M/F 16 (2.3%) 0 (0%) 2 (4.1%) 14 (2.4%)
Age 49 (38, 58) 47 (35, 53) 40 (33, 52) 50 (39, 59) 0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 21 (3.0%) 4 (7.5%) 2 (4.1%) 15 (2.6%)
    ≥25-<35 107 (16%) 9 (17%) 13 (27%) 85 (14%)
    ≥35-<45 148 (21%) 10 (19%) 15 (31%) 123 (21%)
    ≥45-<55 174 (25%) 20 (38%) 10 (20%) 144 (24%)
    ≥55-<80 233 (34%) 10 (19%) 9 (18%) 214 (36%)
    ≥80 7 (1.0%) 0 (0%) 0 (0%) 7 (1.2%)
WHO region (origin)



<0.001
    WHO Africa 206 (31%) 5 (9.8%) 4 (8.2%) 197 (35%)
    WHO Americas 36 (5.4%) 2 (3.9%) 5 (10%) 29 (5.1%)
    WHO Eastern Mediterranean 6 (0.9%) 0 (0%) 1 (2.0%) 5 (0.9%)
    WHO Europe 419 (62%) 44 (86%) 39 (80%) 336 (59%)
    WHO South-East Asia 3 (0.4%) 0 (0%) 0 (0%) 3 (0.5%)
    WHO Western Pacific 1 (0.1%) 0 (0%) 0 (0%) 1 (0.2%)
Primo-infection



<0.001
    Non 578 (84%) 35 (66%) 36 (73%) 507 (86%)
    Oui 112 (16%) 18 (34%) 13 (27%) 81 (14%)
Transmission risk




    Bisexual 45 (6.5%) 6 (11%) 7 (14%) 32 (5.4%)
    Blood 11 (1.6%) 0 (0%) 1 (2.0%) 10 (1.7%)
    Heterosexual 356 (52%) 18 (34%) 13 (27%) 325 (55%)
    IDU 39 (5.7%) 2 (3.8%) 1 (2.0%) 36 (6.1%)
    Mother to child transmission 8 (1.2%) 0 (0%) 0 (0%) 8 (1.4%)
    MSM 203 (29%) 26 (49%) 26 (53%) 151 (26%)
    Others 6 (0.9%) 0 (0%) 0 (0%) 6 (1.0%)
    Unknown 22 (3.2%) 1 (1.9%) 1 (2.0%) 20 (3.4%)
Drug use




    Current 51 (11%) 7 (16%) 7 (18%) 37 (9.4%)
    None 309 (65%) 25 (56%) 23 (58%) 261 (66%)
    Past 47 (9.8%) 10 (22%) 4 (10%) 33 (8.4%)
    Sometimes 18 (3.8%) 1 (2.2%) 3 (7.5%) 14 (3.6%)
    Substitution 21 (4.4%) 1 (2.2%) 0 (0%) 20 (5.1%)
    Unknown 33 (6.9%) 1 (2.2%) 3 (7.5%) 29 (7.4%)
Baseline HIV RNA level (log10) 4.78 (3.87, 5.53) 5.32 (4.40, 6.28) 4.91 (4.25, 5.46) 4.75 (3.80, 5.50) 0.017
Baseline CD4 count 353 (180, 575) 477 (306, 631) 415 (254, 582) 326 (149, 561) 0.004
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 588
1
Not Growing
N = 100
1
Growing
N = 2
1
p-value2
sex


<0.001
    Female 229 (39%) 13 (13%) 0 (0%)
    Male 344 (59%) 85 (85%) 2 (100%)
    Transgender F/M 1 (0.2%) 0 (0%) 0 (0%)
    Transgender M/F 14 (2.4%) 2 (2.0%) 0 (0%)
Age 50 (39, 59) 43 (33, 53) 56 (46, 65) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 15 (2.6%) 6 (6.0%) 0 (0%)
    ≥25-<35 85 (14%) 22 (22%) 0 (0%)
    ≥35-<45 123 (21%) 25 (25%) 0 (0%)
    ≥45-<55 144 (24%) 29 (29%) 1 (50%)
    ≥55-<80 214 (36%) 18 (18%) 1 (50%)
    ≥80 7 (1.2%) 0 (0%) 0 (0%)
WHO region (origin)


<0.001
    WHO Africa 197 (35%) 9 (9.2%) 0 (0%)
    WHO Americas 29 (5.1%) 7 (7.1%) 0 (0%)
    WHO Eastern Mediterranean 5 (0.9%) 1 (1.0%) 0 (0%)
    WHO Europe 336 (59%) 81 (83%) 2 (100%)
    WHO South-East Asia 3 (0.5%) 0 (0%) 0 (0%)
    WHO Western Pacific 1 (0.2%) 0 (0%) 0 (0%)
Primo-infection


<0.001
    Non 507 (86%) 69 (69%) 2 (100%)
    Oui 81 (14%) 31 (31%) 0 (0%)
Transmission risk



    Bisexual 32 (5.4%) 13 (13%) 0 (0%)
    Blood 10 (1.7%) 1 (1.0%) 0 (0%)
    Heterosexual 325 (55%) 31 (31%) 0 (0%)
    IDU 36 (6.1%) 2 (2.0%) 1 (50%)
    Mother to child transmission 8 (1.4%) 0 (0%) 0 (0%)
    MSM 151 (26%) 51 (51%) 1 (50%)
    Others 6 (1.0%) 0 (0%) 0 (0%)
    Unknown 20 (3.4%) 2 (2.0%) 0 (0%)
Drug use



    Current 37 (9.4%) 13 (16%) 1 (50%)
    None 261 (66%) 48 (58%) 0 (0%)
    Past 33 (8.4%) 14 (17%) 0 (0%)
    Sometimes 14 (3.6%) 4 (4.8%) 0 (0%)
    Substitution 20 (5.1%) 0 (0%) 1 (50%)
    Unknown 29 (7.4%) 4 (4.8%) 0 (0%)
Baseline HIV RNA level (log10) 4.75 (3.80, 5.50) 5.07 (4.30, 5.79) NA (NA, NA) 0.012
Baseline CD4 count 326 (149, 561) 474 (291, 601) NA (NA, NA) 0.001
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 53
1
Not clustering
N = 588
1
spread
N = 49
1
p-value2
sex


<0.001
    Female 5 (9.4%) 229 (39%) 8 (16%)
    Male 48 (91%) 344 (59%) 39 (80%)
    Transgender F/M 0 (0%) 1 (0.2%) 0 (0%)
    Transgender M/F 0 (0%) 14 (2.4%) 2 (4.1%)
Age 41 (32, 53) 50 (39, 59) 46 (34, 54) 0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 6 (11%) 15 (2.6%) 0 (0%)
    ≥25-<35 9 (17%) 85 (14%) 13 (27%)
    ≥35-<45 15 (28%) 123 (21%) 10 (20%)
    ≥45-<55 14 (26%) 144 (24%) 16 (33%)
    ≥55-<80 9 (17%) 214 (36%) 10 (20%)
    ≥80 0 (0%) 7 (1.2%) 0 (0%)
WHO region (origin)


<0.001
    WHO Africa 4 (7.7%) 197 (35%) 5 (10%)
    WHO Americas 1 (1.9%) 29 (5.1%) 6 (13%)
    WHO Eastern Mediterranean 0 (0%) 5 (0.9%) 1 (2.1%)
    WHO Europe 47 (90%) 336 (59%) 36 (75%)
    WHO South-East Asia 0 (0%) 3 (0.5%) 0 (0%)
    WHO Western Pacific 0 (0%) 1 (0.2%) 0 (0%)
Primo-infection


<0.001
    Non 33 (62%) 507 (86%) 38 (78%)
    Oui 20 (38%) 81 (14%) 11 (22%)
Transmission risk



    Bisexual 9 (17%) 32 (5.4%) 4 (8.2%)
    Blood 0 (0%) 10 (1.7%) 1 (2.0%)
    Heterosexual 13 (25%) 325 (55%) 18 (37%)
    IDU 1 (1.9%) 36 (6.1%) 2 (4.1%)
    Mother to child transmission 0 (0%) 8 (1.4%) 0 (0%)
    MSM 28 (53%) 151 (26%) 24 (49%)
    Others 0 (0%) 6 (1.0%) 0 (0%)
    Unknown 2 (3.8%) 20 (3.4%) 0 (0%)
Drug use



    Current 8 (19%) 37 (9.4%) 6 (14%)
    None 25 (58%) 261 (66%) 23 (55%)
    Past 7 (16%) 33 (8.4%) 7 (17%)
    Sometimes 2 (4.7%) 14 (3.6%) 2 (4.8%)
    Substitution 0 (0%) 20 (5.1%) 1 (2.4%)
    Unknown 1 (2.3%) 29 (7.4%) 3 (7.1%)
Baseline HIV RNA level (log10) 5.00 (4.28, 5.46) 4.75 (3.80, 5.50) 5.33 (4.36, 5.85) 0.034
Baseline CD4 count 476 (319, 607) 326 (149, 561) 435 (245, 572) 0.004
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Guadeloupe

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 91/645, i.e. 14%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 186 distinct clusters including 30% of local clusters ( 5 600% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 645
1
Clusters size ≥3
N = 47
1
Dyads
N = 44
1
Singletons
N = 554
1
p-value2
sex



<0.001
    Female 240 (37%) 2 (4.3%) 14 (32%) 224 (40%)
    Male 405 (63%) 45 (96%) 30 (68%) 330 (60%)
Age 50 (38, 60) 34 (27, 47) 40 (33, 53) 51 (41, 60) <0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 29 (4.5%) 6 (13%) 3 (6.8%) 20 (3.6%)
    ≥25-<35 100 (16%) 19 (40%) 10 (23%) 71 (13%)
    ≥35-<45 110 (17%) 7 (15%) 13 (30%) 90 (16%)
    ≥45-<55 169 (26%) 10 (21%) 9 (20%) 150 (27%)
    ≥55-<80 223 (35%) 5 (11%) 9 (20%) 209 (38%)
    ≥80 14 (2.2%) 0 (0%) 0 (0%) 14 (2.5%)
WHO region (origin)



<0.001
    WHO Africa 4 (0.6%) 0 (0%) 0 (0%) 4 (0.7%)
    WHO Americas 232 (36%) 4 (8.5%) 7 (16%) 221 (40%)
    WHO Eastern Mediterranean 2 (0.3%) 0 (0%) 0 (0%) 2 (0.4%)
    WHO Europe 399 (62%) 43 (91%) 37 (84%) 319 (58%)
    WHO South-East Asia 1 (0.2%) 0 (0%) 0 (0%) 1 (0.2%)
    WHO Western Pacific 1 (0.2%) 0 (0%) 0 (0%) 1 (0.2%)
Primo-infection



<0.001
    Non 616 (96%) 38 (81%) 42 (95%) 536 (97%)
    Oui 29 (4.5%) 9 (19%) 2 (4.5%) 18 (3.2%)
Transmission risk




    Bisexual 41 (6.4%) 7 (15%) 5 (11%) 29 (5.2%)
    Blood 5 (0.8%) 0 (0%) 0 (0%) 5 (0.9%)
    Heterosexual 470 (73%) 17 (36%) 27 (61%) 426 (77%)
    IDU 7 (1.1%) 0 (0%) 0 (0%) 7 (1.3%)
    Mother to child transmission 6 (0.9%) 0 (0%) 0 (0%) 6 (1.1%)
    MSM 101 (16%) 22 (47%) 12 (27%) 67 (12%)
    Others 1 (0.2%) 0 (0%) 0 (0%) 1 (0.2%)
    Unknown 14 (2.2%) 1 (2.1%) 0 (0%) 13 (2.3%)
Drug use




    Current 44 (7.8%) 7 (17%) 5 (14%) 32 (6.6%)
    None 425 (75%) 30 (71%) 27 (75%) 368 (76%)
    Past 45 (8.0%) 0 (0%) 1 (2.8%) 44 (9.0%)
    Sometimes 17 (3.0%) 3 (7.1%) 2 (5.6%) 12 (2.5%)
    Substitution 2 (0.4%) 0 (0%) 0 (0%) 2 (0.4%)
    Unknown 32 (5.7%) 2 (4.8%) 1 (2.8%) 29 (6.0%)
Baseline HIV RNA level (log10) 4.67 (4.07, 5.16) 4.73 (4.05, 4.95) 4.69 (4.28, 5.32) 4.67 (4.06, 5.16) 0.7
Baseline CD4 count 332 (148, 495) 406 (295, 575) 413 (274, 515) 323 (132, 486) 0.013
1 n (%); Median (Q1, Q3)
2 Pearson’s Chi-squared test; Kruskal-Wallis rank sum test; Fisher’s exact test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 554
1
Not Growing
N = 90
1
Growing
N = 1
1
p-value2
sex


<0.001
    Female 224 (40%) 16 (18%) 0 (0%)
    Male 330 (60%) 74 (82%) 1 (100%)
Age 51 (41, 60) 37 (29, 48) 60 (60, 60) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 20 (3.6%) 9 (10%) 0 (0%)
    ≥25-<35 71 (13%) 29 (32%) 0 (0%)
    ≥35-<45 90 (16%) 20 (22%) 0 (0%)
    ≥45-<55 150 (27%) 19 (21%) 0 (0%)
    ≥55-<80 209 (38%) 13 (14%) 1 (100%)
    ≥80 14 (2.5%) 0 (0%) 0 (0%)
WHO region (origin)


<0.001
    WHO Africa 4 (0.7%) 0 (0%) 0 (0%)
    WHO Americas 221 (40%) 11 (12%) 0 (0%)
    WHO Eastern Mediterranean 2 (0.4%) 0 (0%) 0 (0%)
    WHO Europe 319 (58%) 79 (88%) 1 (100%)
    WHO South-East Asia 1 (0.2%) 0 (0%) 0 (0%)
    WHO Western Pacific 1 (0.2%) 0 (0%) 0 (0%)
Primo-infection


0.002
    Non 536 (97%) 79 (88%) 1 (100%)
    Oui 18 (3.2%) 11 (12%) 0 (0%)
Transmission risk



    Bisexual 29 (5.2%) 12 (13%) 0 (0%)
    Blood 5 (0.9%) 0 (0%) 0 (0%)
    Heterosexual 426 (77%) 44 (49%) 0 (0%)
    IDU 7 (1.3%) 0 (0%) 0 (0%)
    Mother to child transmission 6 (1.1%) 0 (0%) 0 (0%)
    MSM 67 (12%) 33 (37%) 1 (100%)
    Others 1 (0.2%) 0 (0%) 0 (0%)
    Unknown 13 (2.3%) 1 (1.1%) 0 (0%)
Drug use


0.015
    Current 32 (6.6%) 12 (16%) 0 (0%)
    None 368 (76%) 56 (73%) 1 (100%)
    Past 44 (9.0%) 1 (1.3%) 0 (0%)
    Sometimes 12 (2.5%) 5 (6.5%) 0 (0%)
    Substitution 2 (0.4%) 0 (0%) 0 (0%)
    Unknown 29 (6.0%) 3 (3.9%) 0 (0%)
Baseline HIV RNA level (log10) 4.67 (4.06, 5.16) 4.71 (4.25, 5.18) NA (NA, NA) 0.7
Baseline CD4 count 323 (132, 486) 408 (290, 549) NA (NA, NA) 0.005
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 56
1
Not clustering
N = 554
1
spread
N = 35
1
p-value2
sex


<0.001
    Female 12 (21%) 224 (40%) 4 (11%)
    Male 44 (79%) 330 (60%) 31 (89%)
Age 39 (31, 50) 51 (41, 60) 35 (27, 46) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 6 (11%) 20 (3.6%) 3 (8.6%)
    ≥25-<35 15 (27%) 71 (13%) 14 (40%)
    ≥35-<45 11 (20%) 90 (16%) 9 (26%)
    ≥45-<55 15 (27%) 150 (27%) 4 (11%)
    ≥55-<80 9 (16%) 209 (38%) 5 (14%)
    ≥80 0 (0%) 14 (2.5%) 0 (0%)
WHO region (origin)


<0.001
    WHO Africa 0 (0%) 4 (0.7%) 0 (0%)
    WHO Americas 7 (13%) 221 (40%) 4 (11%)
    WHO Eastern Mediterranean 0 (0%) 2 (0.4%) 0 (0%)
    WHO Europe 49 (88%) 319 (58%) 31 (89%)
    WHO South-East Asia 0 (0%) 1 (0.2%) 0 (0%)
    WHO Western Pacific 0 (0%) 1 (0.2%) 0 (0%)
Primo-infection


<0.001
    Non 53 (95%) 536 (97%) 27 (77%)
    Oui 3 (5.4%) 18 (3.2%) 8 (23%)
Transmission risk



    Bisexual 7 (13%) 29 (5.2%) 5 (14%)
    Blood 0 (0%) 5 (0.9%) 0 (0%)
    Heterosexual 32 (57%) 426 (77%) 12 (34%)
    IDU 0 (0%) 7 (1.3%) 0 (0%)
    Mother to child transmission 0 (0%) 6 (1.1%) 0 (0%)
    MSM 17 (30%) 67 (12%) 17 (49%)
    Others 0 (0%) 1 (0.2%) 0 (0%)
    Unknown 0 (0%) 13 (2.3%) 1 (2.9%)
Drug use



    Current 6 (13%) 32 (6.6%) 6 (19%)
    None 37 (80%) 368 (76%) 20 (63%)
    Past 0 (0%) 44 (9.0%) 1 (3.1%)
    Sometimes 1 (2.2%) 12 (2.5%) 4 (13%)
    Substitution 0 (0%) 2 (0.4%) 0 (0%)
    Unknown 2 (4.3%) 29 (6.0%) 1 (3.1%)
Baseline HIV RNA level (log10) 4.69 (4.01, 5.21) 4.67 (4.06, 5.16) 4.75 (4.40, 5.17) 0.8
Baseline CD4 count 349 (288, 491) 323 (132, 486) 448 (295, 575) 0.013
1 n (%); Median (Q1, Q3)
2 Pearson’s Chi-squared test; Kruskal-Wallis rank sum test; Fisher’s exact test

Auvergne-Rhône-Alpes

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 37/303, i.e. 12%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 219 distinct clusters including 6% of local clusters ( 1 400% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 303
1
Clusters size ≥3
N = 23
1
Dyads
N = 14
1
Singletons
N = 266
1
p-value2
sex



0.011
    Female 98 (32%) 1 (4.3%) 5 (36%) 92 (35%)
    Male 204 (67%) 22 (96%) 9 (64%) 173 (65%)
    Transgender M/F 1 (0.3%) 0 (0%) 0 (0%) 1 (0.4%)
Age 49 (38, 58) 44 (35, 52) 40 (31, 48) 50 (39, 59) 0.005
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 4 (1.3%) 0 (0%) 0 (0%) 4 (1.5%)
    ≥25-<35 47 (16%) 4 (17%) 5 (36%) 38 (14%)
    ≥35-<45 75 (25%) 8 (35%) 4 (29%) 63 (24%)
    ≥45-<55 77 (25%) 7 (30%) 5 (36%) 65 (24%)
    ≥55-<80 95 (31%) 4 (17%) 0 (0%) 91 (34%)
    ≥80 5 (1.7%) 0 (0%) 0 (0%) 5 (1.9%)
WHO region (origin)



0.4
    WHO Africa 65 (22%) 1 (4.5%) 3 (21%) 61 (24%)
    WHO Americas 9 (3.1%) 0 (0%) 1 (7.1%) 8 (3.1%)
    WHO Eastern Mediterranean 5 (1.7%) 0 (0%) 0 (0%) 5 (2.0%)
    WHO Europe 209 (72%) 21 (95%) 10 (71%) 178 (70%)
    WHO South-East Asia 1 (0.3%) 0 (0%) 0 (0%) 1 (0.4%)
    WHO Western Pacific 2 (0.7%) 0 (0%) 0 (0%) 2 (0.8%)
Primo-infection



0.3
    Non 255 (84%) 17 (74%) 13 (93%) 225 (85%)
    Oui 48 (16%) 6 (26%) 1 (7.1%) 41 (15%)
Transmission risk




    Bisexual 24 (7.9%) 5 (22%) 0 (0%) 19 (7.1%)
    Blood 6 (2.0%) 0 (0%) 0 (0%) 6 (2.3%)
    Heterosexual 127 (42%) 2 (8.7%) 6 (43%) 119 (45%)
    IDU 8 (2.6%) 0 (0%) 0 (0%) 8 (3.0%)
    Mother to child transmission 9 (3.0%) 0 (0%) 0 (0%) 9 (3.4%)
    MSM 117 (39%) 16 (70%) 8 (57%) 93 (35%)
    Others 1 (0.3%) 0 (0%) 0 (0%) 1 (0.4%)
    Unknown 11 (3.6%) 0 (0%) 0 (0%) 11 (4.1%)
Drug use



0.3
    Current 40 (14%) 6 (27%) 2 (14%) 32 (13%)
    None 190 (66%) 11 (50%) 10 (71%) 169 (67%)
    Past 36 (13%) 1 (4.5%) 2 (14%) 33 (13%)
    Sometimes 8 (2.8%) 2 (9.1%) 0 (0%) 6 (2.4%)
    Substitution 4 (1.4%) 0 (0%) 0 (0%) 4 (1.6%)
    Unknown 10 (3.5%) 2 (9.1%) 0 (0%) 8 (3.2%)
Baseline HIV RNA level (log10) 4.65 (3.98, 5.26) 4.77 (4.16, 5.66) 4.33 (4.08, 4.34) 4.67 (3.85, 5.27) 0.4
Baseline CD4 count 442 (270, 638) 639 (531, 778) 517 (431, 609) 417 (258, 618) 0.015
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 266
1
Not Growing
N = 36
1
Growing
N = 1
1
p-value2
sex


0.11
    Female 92 (35%) 6 (17%) 0 (0%)
    Male 173 (65%) 30 (83%) 1 (100%)
    Transgender M/F 1 (0.4%) 0 (0%) 0 (0%)
Age 50 (39, 59) 40 (35, 49) 63 (63, 63) 0.002
Age group


0.023
    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 4 (1.5%) 0 (0%) 0 (0%)
    ≥25-<35 38 (14%) 9 (25%) 0 (0%)
    ≥35-<45 63 (24%) 12 (33%) 0 (0%)
    ≥45-<55 65 (24%) 12 (33%) 0 (0%)
    ≥55-<80 91 (34%) 3 (8.3%) 1 (100%)
    ≥80 5 (1.9%) 0 (0%) 0 (0%)
WHO region (origin)


0.6
    WHO Africa 61 (24%) 4 (11%) 0 (0%)
    WHO Americas 8 (3.1%) 1 (2.9%) 0 (0%)
    WHO Eastern Mediterranean 5 (2.0%) 0 (0%) 0 (0%)
    WHO Europe 178 (70%) 30 (86%) 1 (100%)
    WHO South-East Asia 1 (0.4%) 0 (0%) 0 (0%)
    WHO Western Pacific 2 (0.8%) 0 (0%) 0 (0%)
Primo-infection


0.2
    Non 225 (85%) 30 (83%) 0 (0%)
    Oui 41 (15%) 6 (17%) 1 (100%)
Transmission risk


0.041
    Bisexual 19 (7.1%) 5 (14%) 0 (0%)
    Blood 6 (2.3%) 0 (0%) 0 (0%)
    Heterosexual 119 (45%) 8 (22%) 0 (0%)
    IDU 8 (3.0%) 0 (0%) 0 (0%)
    Mother to child transmission 9 (3.4%) 0 (0%) 0 (0%)
    MSM 93 (35%) 23 (64%) 1 (100%)
    Others 1 (0.4%) 0 (0%) 0 (0%)
    Unknown 11 (4.1%) 0 (0%) 0 (0%)
Drug use


0.5
    Current 32 (13%) 8 (23%) 0 (0%)
    None 169 (67%) 20 (57%) 1 (100%)
    Past 33 (13%) 3 (8.6%) 0 (0%)
    Sometimes 6 (2.4%) 2 (5.7%) 0 (0%)
    Substitution 4 (1.6%) 0 (0%) 0 (0%)
    Unknown 8 (3.2%) 2 (5.7%) 0 (0%)
Baseline HIV RNA level (log10) 4.67 (3.85, 5.27) 4.42 (4.15, 5.26) 4.88 (4.88, 4.88) >0.9
Baseline CD4 count 417 (258, 618) 581 (442, 758) 687 (687, 687) 0.015
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 14
1
Not clustering
N = 266
1
spread
N = 23
1
p-value2
sex


0.2
    Female 2 (14%) 92 (35%) 4 (17%)
    Male 12 (86%) 173 (65%) 19 (83%)
    Transgender M/F 0 (0%) 1 (0.4%) 0 (0%)
Age 48 (35, 52) 50 (39, 59) 40 (34, 45) 0.005
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 0 (0%) 4 (1.5%) 0 (0%)
    ≥25-<35 3 (21%) 38 (14%) 6 (26%)
    ≥35-<45 3 (21%) 63 (24%) 9 (39%)
    ≥45-<55 6 (43%) 65 (24%) 6 (26%)
    ≥55-<80 2 (14%) 91 (34%) 2 (8.7%)
    ≥80 0 (0%) 5 (1.9%) 0 (0%)
WHO region (origin)


0.5
    WHO Africa 0 (0%) 61 (24%) 4 (18%)
    WHO Americas 0 (0%) 8 (3.1%) 1 (4.5%)
    WHO Eastern Mediterranean 0 (0%) 5 (2.0%) 0 (0%)
    WHO Europe 14 (100%) 178 (70%) 17 (77%)
    WHO South-East Asia 0 (0%) 1 (0.4%) 0 (0%)
    WHO Western Pacific 0 (0%) 2 (0.8%) 0 (0%)
Primo-infection


0.4
    Non 10 (71%) 225 (85%) 20 (87%)
    Oui 4 (29%) 41 (15%) 3 (13%)
Transmission risk


0.2
    Bisexual 2 (14%) 19 (7.1%) 3 (13%)
    Blood 0 (0%) 6 (2.3%) 0 (0%)
    Heterosexual 2 (14%) 119 (45%) 6 (26%)
    IDU 0 (0%) 8 (3.0%) 0 (0%)
    Mother to child transmission 0 (0%) 9 (3.4%) 0 (0%)
    MSM 10 (71%) 93 (35%) 14 (61%)
    Others 0 (0%) 1 (0.4%) 0 (0%)
    Unknown 0 (0%) 11 (4.1%) 0 (0%)
Drug use


0.3
    Current 2 (14%) 32 (13%) 6 (27%)
    None 11 (79%) 169 (67%) 10 (45%)
    Past 1 (7.1%) 33 (13%) 2 (9.1%)
    Sometimes 0 (0%) 6 (2.4%) 2 (9.1%)
    Substitution 0 (0%) 4 (1.6%) 0 (0%)
    Unknown 0 (0%) 8 (3.2%) 2 (9.1%)
Baseline HIV RNA level (log10) 4.50 (4.15, 5.44) 4.67 (3.85, 5.27) 4.46 (4.17, 4.99) 0.9
Baseline CD4 count 580 (517, 667) 417 (258, 618) 637 (414, 789) 0.018
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Martinique

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 174/922, i.e. 19%.

Cluster size and composition

With a genetic distance threshold of 0.5% , we identified 299 distinct clusters including 39% of local clusters ( 11 800% ).

Overall

By origin

Demographics by clustering status

Characteristic Overall
N = 922
1
Clusters size ≥3
N = 99
1
Dyads
N = 75
1
Singletons
N = 748
1
p-value2
sex



0.12
    Female 318 (34%) 27 (27%) 20 (27%) 271 (36%)
    Male 599 (65%) 72 (73%) 54 (72%) 473 (63%)
    Transgender M/F 5 (0.5%) 0 (0%) 1 (1.3%) 4 (0.5%)
Age 53 (40, 63) 37 (30, 53) 45 (33, 56) 55 (43, 64) <0.001
Age group




    <15 0 (0%) 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 32 (3.5%) 10 (10%) 7 (9.3%) 15 (2.0%)
    ≥25-<35 123 (13%) 34 (34%) 14 (19%) 75 (10%)
    ≥35-<45 145 (16%) 18 (18%) 14 (19%) 113 (15%)
    ≥45-<55 182 (20%) 15 (15%) 17 (23%) 150 (20%)
    ≥55-<80 413 (45%) 22 (22%) 23 (31%) 368 (49%)
    ≥80 27 (2.9%) 0 (0%) 0 (0%) 27 (3.6%)
WHO region (origin)



0.004
    WHO Africa 13 (1.5%) 0 (0%) 4 (5.6%) 9 (1.2%)
    WHO Americas 121 (14%) 5 (5.3%) 9 (13%) 107 (15%)
    WHO Eastern Mediterranean 2 (0.2%) 1 (1.1%) 0 (0%) 1 (0.1%)
    WHO Europe 751 (85%) 88 (94%) 59 (82%) 604 (84%)
Primo-infection



<0.001
    Non 851 (92%) 80 (81%) 66 (88%) 705 (94%)
    Oui 71 (7.7%) 19 (19%) 9 (12%) 43 (5.7%)
Transmission risk




    Bisexual 126 (14%) 22 (22%) 11 (15%) 93 (12%)
    Blood 9 (1.0%) 1 (1.0%) 0 (0%) 8 (1.1%)
    Heterosexual 588 (64%) 50 (51%) 32 (43%) 506 (68%)
    IDU 14 (1.5%) 1 (1.0%) 4 (5.3%) 9 (1.2%)
    Mother to child transmission 3 (0.3%) 0 (0%) 0 (0%) 3 (0.4%)
    MSM 169 (18%) 25 (25%) 27 (36%) 117 (16%)
    Others 1 (0.1%) 0 (0%) 1 (1.3%) 0 (0%)
    Unknown 12 (1.3%) 0 (0%) 0 (0%) 12 (1.6%)
Drug use




    Current 108 (13%) 18 (20%) 7 (10%) 83 (12%)
    None 595 (70%) 54 (60%) 45 (65%) 496 (71%)
    Past 124 (14%) 14 (16%) 13 (19%) 97 (14%)
    Sometimes 16 (1.9%) 4 (4.4%) 1 (1.4%) 11 (1.6%)
    Substitution 4 (0.5%) 0 (0%) 1 (1.4%) 3 (0.4%)
    Unknown 9 (1.1%) 0 (0%) 2 (2.9%) 7 (1.0%)
Baseline HIV RNA level (log10) 4.53 (3.94, 5.10) 4.37 (4.04, 5.05) 4.44 (3.96, 5.06) 4.55 (3.93, 5.13) 0.5
Baseline CD4 count 393 (208, 572) 452 (317, 629) 417 (246, 653) 378 (187, 556) 0.007
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test; Pearson’s Chi-squared test

Growing clusters

New clustering individuals

Table of growing clusters

Characteristic Not Clustering
N = 748
1
Not Growing
N = 159
1
Growing
N = 15
1
p-value2
sex


0.093
    Female 271 (36%) 41 (26%) 6 (40%)
    Male 473 (63%) 117 (74%) 9 (60%)
    Transgender M/F 4 (0.5%) 1 (0.6%) 0 (0%)
Age 55 (43, 64) 38 (30, 53) 62 (51, 67) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 15 (2.0%) 17 (11%) 0 (0%)
    ≥25-<35 75 (10%) 48 (30%) 0 (0%)
    ≥35-<45 113 (15%) 32 (20%) 0 (0%)
    ≥45-<55 150 (20%) 27 (17%) 5 (33%)
    ≥55-<80 368 (49%) 35 (22%) 10 (67%)
    ≥80 27 (3.6%) 0 (0%) 0 (0%)
WHO region (origin)


0.11
    WHO Africa 9 (1.2%) 4 (2.6%) 0 (0%)
    WHO Americas 107 (15%) 14 (9.2%) 0 (0%)
    WHO Eastern Mediterranean 1 (0.1%) 1 (0.7%) 0 (0%)
    WHO Europe 604 (84%) 133 (88%) 14 (100%)
Primo-infection


<0.001
    Non 705 (94%) 132 (83%) 14 (93%)
    Oui 43 (5.7%) 27 (17%) 1 (6.7%)
Transmission risk



    Bisexual 93 (12%) 31 (19%) 2 (13%)
    Blood 8 (1.1%) 1 (0.6%) 0 (0%)
    Heterosexual 506 (68%) 70 (44%) 12 (80%)
    IDU 9 (1.2%) 4 (2.5%) 1 (6.7%)
    Mother to child transmission 3 (0.4%) 0 (0%) 0 (0%)
    MSM 117 (16%) 52 (33%) 0 (0%)
    Others 0 (0%) 1 (0.6%) 0 (0%)
    Unknown 12 (1.6%) 0 (0%) 0 (0%)
Drug use



    Current 83 (12%) 24 (17%) 1 (6.7%)
    None 496 (71%) 88 (61%) 11 (73%)
    Past 97 (14%) 24 (17%) 3 (20%)
    Sometimes 11 (1.6%) 5 (3.5%) 0 (0%)
    Substitution 3 (0.4%) 1 (0.7%) 0 (0%)
    Unknown 7 (1.0%) 2 (1.4%) 0 (0%)
Baseline HIV RNA level (log10) 4.55 (3.93, 5.13) 4.35 (3.92, 4.99) 4.83 (4.14, 5.47) 0.13
Baseline CD4 count 378 (187, 556) 429 (305, 636) 373 (267, 599) 0.009
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test

Table of cluster dispersal

Characteristic local only
N = 118
1
Not clustering
N = 748
1
spread
N = 56
1
p-value2
sex


0.11
    Female 29 (25%) 271 (36%) 18 (32%)
    Male 88 (75%) 473 (63%) 38 (68%)
    Transgender M/F 1 (0.8%) 4 (0.5%) 0 (0%)
Age 40 (31, 56) 55 (43, 64) 42 (30, 55) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 8 (6.8%) 15 (2.0%) 9 (16%)
    ≥25-<35 37 (31%) 75 (10%) 11 (20%)
    ≥35-<45 21 (18%) 113 (15%) 11 (20%)
    ≥45-<55 21 (18%) 150 (20%) 11 (20%)
    ≥55-<80 31 (26%) 368 (49%) 14 (25%)
    ≥80 0 (0%) 27 (3.6%) 0 (0%)
WHO region (origin)


0.014
    WHO Africa 3 (2.6%) 9 (1.2%) 1 (2.0%)
    WHO Americas 13 (11%) 107 (15%) 1 (2.0%)
    WHO Eastern Mediterranean 0 (0%) 1 (0.1%) 1 (2.0%)
    WHO Europe 99 (86%) 604 (84%) 48 (94%)
Primo-infection


<0.001
    Non 97 (82%) 705 (94%) 49 (88%)
    Oui 21 (18%) 43 (5.7%) 7 (13%)
Transmission risk



    Bisexual 24 (20%) 93 (12%) 9 (16%)
    Blood 0 (0%) 8 (1.1%) 1 (1.8%)
    Heterosexual 54 (46%) 506 (68%) 28 (50%)
    IDU 3 (2.5%) 9 (1.2%) 2 (3.6%)
    Mother to child transmission 0 (0%) 3 (0.4%) 0 (0%)
    MSM 36 (31%) 117 (16%) 16 (29%)
    Others 1 (0.8%) 0 (0%) 0 (0%)
    Unknown 0 (0%) 12 (1.6%) 0 (0%)
Drug use



    Current 18 (17%) 83 (12%) 7 (13%)
    None 62 (58%) 496 (71%) 37 (70%)
    Past 18 (17%) 97 (14%) 9 (17%)
    Sometimes 5 (4.7%) 11 (1.6%) 0 (0%)
    Substitution 1 (0.9%) 3 (0.4%) 0 (0%)
    Unknown 2 (1.9%) 7 (1.0%) 0 (0%)
Baseline HIV RNA level (log10) 4.35 (3.92, 5.05) 4.55 (3.93, 5.13) 4.64 (4.07, 5.08) 0.4
Baseline CD4 count 420 (288, 617) 378 (187, 556) 449 (310, 643) 0.009
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Kruskal-Wallis rank sum test